read.spike               package:CALIB               R Documentation

_R_e_a_d _S_p_i_k_e_L_i_s_t _f_r_o_m _a _R_G_L_i_s_t__C_A_L_I_B _a_n_d _C_o_n_c_e_n_t_r_a_t_i_o_n _f_i_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Reads a SpikeList from a given RGList_CALIB object and user
     specified concentration files

_U_s_a_g_e:

     read.spike(RG, file = NULL, path = NULL, ext = NULL, sep = "\t", conccol,
                regexpcol, different = FALSE, ...)

_A_r_g_u_m_e_n_t_s:

      RG: a 'RGList_CALIB' object.

    file: character string giving the name of the concentration file.

    path: character string giving the directory containing the file.
          Can be omitted if the file is in the current working
          directory.

     ext: character string giving optional extension to be added to
          each file name.

     sep: field separator character.

 conccol: list with fields 'RConc', 'GConc' giving the column names to
          be used for red and green concentration in the concentration
          file.

regexpcol: character vector giving regular expressions in the 
          concentration file.

different: a logical value. 'TRUE' means that different arrays use 
          different spikes. So every array should have one
          concentration file.  'FALSE' means that different arrays use
          the same spike and only one  concentration file is needed.
          Default is 'FALSE'.

     ...: any other arguments are passed to 'read.table'. 

_D_e_t_a_i_l_s:

     This is the function to generate SpikeList in the CALIB package.
     SpikeList  contains all the information for the spikes. This
     function exacts foreground  and background intensities and spot
     area from RGList_CALIB, which is generated from  funtion
     'read.rg'. Also this funtion reads concentrations  for each spike
     from a user-specified concentration file (or more than one 
     concentration files if different arrays use different spikes).

     For the concentration file, it should contain the following
     columns: regular expression, red and green concentrations and
     spike type. Spike type should be in the set of 'Calibration',
      'Ratio' and 'Negative'.

     See the CALIB User's Guide for the example of this function.

_V_a_l_u_e:

     An 'SpikeList' object containing the components

       R: matrix containing the red channel foreground intensities for
          each spot for each array.

       G: matrix containing the green channel foreground intensities
          for each spot for each array.

      Rb: matrix containing the red channel background intensities for
          each spike for each array.

      Gb: matrix containing the green channel background intensities
          for each spike for each array.

   RArea: matrix containing the red spot area for each spike for each
          array.

   GArea: matrix containing the green spot area for each spike for each
          array.

   RConc: matrix containing the red concentration for each spike for
          each array.

   GConc: matrix containing the green concentration for each spike for
          each array.

   genes: data frame containing annotation information about the
          probes,  for example, spike types and IDs and spatial
          positions on the array

_A_u_t_h_o_r(_s):

     Hui Zhao

_R_e_f_e_r_e_n_c_e_s:

     ~put references to the literature/web site here ~

